<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html><head><title></title>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<link rel="stylesheet" type="text/css" href="search.css"/>
<script type="text/javascript" src="search.js"></script>
</head>
<body class="SRPage">
<div id="SRIndex">
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRResult" id="SR_score">
 <div class="SREntry">
  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_score')">score</a>
  <div class="SRChildren">
    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classmoltk_1_1Aligner_1_1TargetPosition.html#a1516be61aa127409e3f89fba58621bd3" target="_parent">moltk::Aligner::TargetPosition::score()</a>
    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classmoltk_1_1Alignment.html#abde767106550bdb46c923146b3629c2f" target="_parent">moltk::Alignment::score()</a>
    <a id="Item0_c2" onkeydown="return searchResults.NavChild(event,0,2)" onkeypress="return searchResults.NavChild(event,0,2)" onkeyup="return searchResults.NavChild(event,0,2)" class="SRScope" href="../classmoltk_1_1MatrixScorer_1_1TargetPosition.html#afbdb8ce801576546721721d21c441398" target="_parent">moltk::MatrixScorer::TargetPosition::score()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_scorer">
 <div class="SREntry">
  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classmoltk_1_1Aligner_1_1Scorer.html" target="_parent">Scorer</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_scorer">
 <div class="SREntry">
  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_scorer')">scorer</a>
  <div class="SRChildren">
    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae" target="_parent">moltk::Aligner::scorer()</a>
    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classmoltk_1_1Aligner_1_1Scorer.html#acdd1d2e2c6d447444eba9155ff92f07b" target="_parent">moltk::Aligner::Scorer::Scorer()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_scores_5fby_5fresidue_5ftype_5findex">
 <div class="SREntry">
  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ab3e868c658e21122068e74ec7eaf5048" target="_parent">scores_by_residue_type_index</a>
  <span class="SRScope">moltk::MatrixScorer::TargetPosition</span>
 </div>
</div>
<div class="SRResult" id="SR_seq1">
 <div class="SREntry">
  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a95bf66d275c37f120f9698a441eaa18b" target="_parent">seq1</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_seq2">
 <div class="SREntry">
  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a934541c902699844d3fbcc4b04e96444" target="_parent">seq2</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_sequence_5findex">
 <div class="SREntry">
  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classmoltk_1_1EString_1_1const__iterator.html#aebfe683ee618731fb3548e2f6a6d16f4" target="_parent">sequence_index</a>
  <span class="SRScope">moltk::EString::const_iterator</span>
 </div>
</div>
<div class="SRResult" id="SR_sequence_5fweight">
 <div class="SREntry">
  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classmoltk_1_1Alignment_1_1Row.html#a4fec4a1fd2d57745a431a9a27482fa8f" target="_parent">sequence_weight</a>
  <span class="SRScope">moltk::Alignment::Row</span>
 </div>
</div>
<div class="SRResult" id="SR_sequences">
 <div class="SREntry">
  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classmoltk_1_1Alignment.html#a78aa4d5f29a114e1a58b7f32eb98e24d" target="_parent">sequences</a>
  <span class="SRScope">moltk::Alignment</span>
 </div>
</div>
<div class="SRResult" id="SR_set_5fend_5fgaps_5ffree">
 <div class="SREntry">
  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_set_5fend_5fgaps_5ffree')">set_end_gaps_free</a>
  <div class="SRChildren">
    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classmoltk_1_1Aligner_1_1Scorer.html#aa163edd66b5c82b40a48803b0df20340" target="_parent">moltk::Aligner::Scorer::set_end_gaps_free()</a>
    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classmoltk_1_1Aligner.html#a1a3475cfc191d9c7efa26f26ba4436b8" target="_parent">moltk::Aligner::set_end_gaps_free()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_set_5ffrom_5fangle_5fabout_5funit_5fvector">
 <div class="SREntry">
  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classmoltk_1_1Rotation3D.html#a93cd577dd17fa9cbf1ba341baeb64ca1" target="_parent">set_from_angle_about_unit_vector</a>
  <span class="SRScope">moltk::Rotation3D</span>
 </div>
</div>
<div class="SRResult" id="SR_set_5ffrom_5fangle_5faxis">
 <div class="SREntry">
  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classmoltk_1_1Quaternion.html#affaf96ecdb1879a5c74ad281d39417f2" target="_parent">set_from_angle_axis</a>
  <span class="SRScope">moltk::Quaternion</span>
 </div>
</div>
<div class="SRResult" id="SR_set_5ffrom_5felements">
 <div class="SREntry">
  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classmoltk_1_1Rotation3D.html#a533ee2bc725541f6dfbf8e8e9769dbc1" target="_parent">set_from_elements</a>
  <span class="SRScope">moltk::Rotation3D</span>
 </div>
</div>
<div class="SRResult" id="SR_set_5ffrom_5fquaternion">
 <div class="SREntry">
  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classmoltk_1_1Rotation3D.html#a7509d7abc00a0349c45992e2471bd562" target="_parent">set_from_quaternion</a>
  <span class="SRScope">moltk::Rotation3D</span>
 </div>
</div>
<div class="SRResult" id="SR_set_5fscore">
 <div class="SREntry">
  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classmoltk_1_1Alignment.html#a110d140d99982b84a8545a23d51b8543" target="_parent">set_score</a>
  <span class="SRScope">moltk::Alignment</span>
 </div>
</div>
<div class="SRResult" id="SR_sin">
 <div class="SREntry">
  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../namespacemoltk_1_1units.html#ac050671e9310a1b41bd10ceef0ffa3be" target="_parent">sin</a>
  <span class="SRScope">moltk::units</span>
 </div>
</div>
<div class="SRResult" id="SR_size">
 <div class="SREntry">
  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_size')">size</a>
  <div class="SRChildren">
    <a id="Item16_c0" onkeydown="return searchResults.NavChild(event,16,0)" onkeypress="return searchResults.NavChild(event,16,0)" onkeyup="return searchResults.NavChild(event,16,0)" class="SRScope" href="../classmoltk_1_1Quaternion.html#aeb9b1be7a1bc9b90140803422c06b05c" target="_parent">moltk::Quaternion::size()</a>
    <a id="Item16_c1" onkeydown="return searchResults.NavChild(event,16,1)" onkeypress="return searchResults.NavChild(event,16,1)" onkeyup="return searchResults.NavChild(event,16,1)" class="SRScope" href="../classmoltk_1_1BaseVector3D.html#ad92f8ef5c2fd9b3c8cb09fce7e1b521b" target="_parent">moltk::BaseVector3D::size() const </a>
    <a id="Item16_c2" onkeydown="return searchResults.NavChild(event,16,2)" onkeypress="return searchResults.NavChild(event,16,2)" onkeyup="return searchResults.NavChild(event,16,2)" class="SRScope" href="../classmoltk_1_1BaseVector3D.html#a3624a981da731d31bae9b31cedebddb1" target="_parent">moltk::BaseVector3D::SIZE()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_size_5ftype">
 <div class="SREntry">
  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_size_5ftype')">size_type</a>
  <div class="SRChildren">
    <a id="Item17_c0" onkeydown="return searchResults.NavChild(event,17,0)" onkeypress="return searchResults.NavChild(event,17,0)" onkeyup="return searchResults.NavChild(event,17,0)" class="SRScope" href="../classmoltk_1_1Quaternion.html#adea988431eacf534b466b34bce0fda5d" target="_parent">moltk::Quaternion::size_type()</a>
    <a id="Item17_c1" onkeydown="return searchResults.NavChild(event,17,1)" onkeypress="return searchResults.NavChild(event,17,1)" onkeyup="return searchResults.NavChild(event,17,1)" class="SRScope" href="../classmoltk_1_1BaseVector3D.html#a946754e9570f3cdedc30b08fc9c7ec25" target="_parent">moltk::BaseVector3D::size_type()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_sqrt">
 <div class="SREntry">
  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../namespacemoltk_1_1units.html#a6bf43e6d5d5ccf3983219f867212f7f6" target="_parent">sqrt</a>
  <span class="SRScope">moltk::units</span>
 </div>
</div>
<div class="SRResult" id="SR_squareroottype">
 <div class="SREntry">
  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_squareroottype')">SquareRootType</a>
  <div class="SRChildren">
    <a id="Item19_c0" onkeydown="return searchResults.NavChild(event,19,0)" onkeypress="return searchResults.NavChild(event,19,0)" onkeyup="return searchResults.NavChild(event,19,0)" class="SRScope" href="../structmoltk_1_1units_1_1Dimension.html#ad234223c7c2dae7fe9d9a7a4cb0ebb7c" target="_parent">moltk::units::Dimension::SquareRootType()</a>
    <a id="Item19_c1" onkeydown="return searchResults.NavChild(event,19,1)" onkeypress="return searchResults.NavChild(event,19,1)" onkeyup="return searchResults.NavChild(event,19,1)" class="SRScope" href="../structmoltk_1_1units_1_1Unit.html#aec3622514f1535f0ff7eef06d83c0de1" target="_parent">moltk::units::Unit::SquareRootType()</a>
    <a id="Item19_c2" onkeydown="return searchResults.NavChild(event,19,2)" onkeypress="return searchResults.NavChild(event,19,2)" onkeyup="return searchResults.NavChild(event,19,2)" class="SRScope" href="../structmoltk_1_1units_1_1Quantity.html#a819bd6379a7cf717890d92d448439bab" target="_parent">moltk::units::Quantity::SquareRootType()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_squaretype">
 <div class="SREntry">
  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_squaretype')">SquareType</a>
  <div class="SRChildren">
    <a id="Item20_c0" onkeydown="return searchResults.NavChild(event,20,0)" onkeypress="return searchResults.NavChild(event,20,0)" onkeyup="return searchResults.NavChild(event,20,0)" class="SRScope" href="../structmoltk_1_1units_1_1Dimension.html#ac9819c45990ae40740d2a68f190bf9d5" target="_parent">moltk::units::Dimension::SquareType()</a>
    <a id="Item20_c1" onkeydown="return searchResults.NavChild(event,20,1)" onkeypress="return searchResults.NavChild(event,20,1)" onkeyup="return searchResults.NavChild(event,20,1)" class="SRScope" href="../structmoltk_1_1units_1_1Unit.html#a11d0f74ab1654292bf50a66aced07fa5" target="_parent">moltk::units::Unit::SquareType()</a>
    <a id="Item20_c2" onkeydown="return searchResults.NavChild(event,20,2)" onkeypress="return searchResults.NavChild(event,20,2)" onkeyup="return searchResults.NavChild(event,20,2)" class="SRScope" href="../structmoltk_1_1units_1_1Quantity.html#ab8db4eeb0cf1adc544fec23c12c0c070" target="_parent">moltk::units::Quantity::SquareType()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_stage">
 <div class="SREntry">
  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208" target="_parent">Stage</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5fallocated">
 <div class="SREntry">
  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abbf7d1ed6268e8d3a7b8725a59b69d9f" target="_parent">STAGE_ALLOCATED</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5fempty">
 <div class="SREntry">
  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a2877fdfe8fa9345c485dc69d2f5200ca" target="_parent">STAGE_EMPTY</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5frecurrence_5fcomputed">
 <div class="SREntry">
  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a22d74955c68c209611ee163f65aa2cc7" target="_parent">STAGE_RECURRENCE_COMPUTED</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5fscorer">
 <div class="SREntry">
  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a42a9835d9845ffd8795ddcf578b20696" target="_parent">STAGE_SCORER</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5fsequence">
 <div class="SREntry">
  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a5ab4a5ba046f6d4b741e687baecbff92" target="_parent">STAGE_SEQUENCE</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5ftable_5finitialized">
 <div class="SREntry">
  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ad21d8375c870feed36071a180c7a797c" target="_parent">STAGE_TABLE_INITIALIZED</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_stage_5ftraced">
 <div class="SREntry">
  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ae27f4f916fb73fc17d2310072d718cb0" target="_parent">STAGE_TRACED</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_structures">
 <div class="SREntry">
  <a id="Item29" onkeydown="return searchResults.Nav(event,29)" onkeypress="return searchResults.Nav(event,29)" onkeyup="return searchResults.Nav(event,29)" class="SRSymbol" href="../classmoltk_1_1Alignment.html#aa6fde73aa22498189439380b2a245f37" target="_parent">structures</a>
  <span class="SRScope">moltk::Alignment</span>
 </div>
</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
<script type="text/javascript"><!--
document.getElementById("Loading").style.display="none";
document.getElementById("NoMatches").style.display="none";
var searchResults = new SearchResults("searchResults");
searchResults.Search();
--></script>
</div>
</body>
</html>
